Michael Lewis has become the latest member of the 49ers to say “thanks, but no thanks” to the Mike Singletary regime.

His agent, Rodney Williams, told Comcast SportsNet that his client will not return to the team, saying: “The relationship is beyond repair. We’ve asked to be released.”

As the 49ers practiced Friday before boarding a flight to Atlanta, Taylor Mays and Reggie Smith were taking reps at strong safety. Lewis, a starter in all 50 games he has played since joining the 49ers in 2007, was not present.

“I told him to go ahead and do what he has to do,” said Singletary, the 49ers’ coach. “As far as if he will make the trip or not, I’m not sure at this point. It depends on if things can be worked out or not. It’s personal reasons, and that’s on Mike. I don’t talk about that. You have to talk to Mike about that.”

According to an NFL Network report Monday, Lewis and linebacker Takeo Spikes were to be benched after the 31-10 loss to the Kansas City Chiefs. But asked about changes in the lineup Wednesday, Singletary said the starters would remain intact.

Lewis, 30, is a nine-year veteran who joined the 49ers as an unrestricted free agent from the Philadelphia Eagles. He agreed this past offseason to accept a substantial pay cut from a reported $4 million to $2 million.

Singletary declined to answer when asked if Lewis’ absence had to do with football or was a family matter, nor would he say if Lewis would start if he went to Atlanta.

“I don’t want to get into if he were here or not,” Singletary said. “All I know is he’s not here for personal reasons.”

Lewis follows the footsteps of defensive lineman Kentwan Balmer and running back Glen Coffee, who also left the team of their own volition.

Balmer, a first-round draft pick in 2008, left the club Aug. 9 and eventually was traded to the Seattle Seahawks for a sixth-round draft pick.

Coffee, a third-round choice in 2009 and the backup to Frank Gore, left the team Aug. 13 and announced his retirement, saying he wanted to focus more on his religious beliefs than on football.

Singletary said the club didn’t have a replacement strategy for Lewis, whether it be plugging in Mays, Smith or a combination of the two.

When Lewis left the Chiefs game for five plays, he was replaced by Smith, who also worked at the position in training camp.

At practice Friday, Mays, a 6-foot-3, 230-pound rookie from USC, got most of the work with the first team.

“The thing is, Reggie has been here for three years, so he has a good feel for what we’re doing,” Singletary said. “Taylor, in case he has to play, whether it’s a sub situation or a base situation, it’s just a matter of him knowing as much as he can, and we want to get him all the reps he possibly can.”

Mays wasn’t eager to discuss his role. He has played only on special teams through three games.

“I haven’t played the first three games on defense, and I don’t know if that’s going to change or not,” Mays said. “We’ll see what happens.”

Smith referred questions about Lewis to Singletary and said, “I just have to be ready for anything.”

That will be a good motto when facing the Falcons on Sunday. Atlanta beat the 49ers 45-10 last season, has the No. 6 offense in the NFL at 385.3 yards per game and has one of the best tight ends in NFL history in Tony Gonzalez.

Wide receiver/returner Ted Ginn Jr. (knee) and center Eric Heitmann (fibula) didn’t practice and are listed as doubtful. Cornerback William James (ankle) was limited and is questionable. Safety Dashon Goldson (knee) and Spikes (knee) are listed as probable.

The 49ers have a 4-11 road record under Singletary, with two of those wins coming against St. Louis and one against Buffalo. When asked about the qualities of a good road team, Singletary said, “I don’t know. I hope to become one of them real soon. I couldn’t answer that.”

One thing that might help — a fast start. In none of the 15 road games under Singletary have the 49ers scored more than seven points in the first quarter.